comapr

comapr detects crossover intervals for single gametes from their haplotype states sequences and stores the crossovers in GRanges object.

Key Features:

• Crossover interval detection: Detects crossover intervals for single gametes from their haplotype states sequences.
• GRanges storage: Stores the detected crossovers in GRanges object.
• Genetic distance calculation: Calculates genetic distances via mapping functions using estimated crossover rates for marker intervals.
• Genetic map visualization: Implements visualization functions for plotting interval-based genetic map.
• Cumulative genetic distance visualization: Implements visualization functions for plotting cumulative genetic distances.

Scientific Applications:

• Crossover landscape analysis: Reveals the variation of crossovers landscapes across the genome and across individuals.
• Genetic map construction: Constructs interval-based genetic maps from estimated crossover rates.

Methodology:

Crossover intervals are detected from haplotype states sequences of single gametes, stored in GRanges object, and genetic distances are calculated via mapping functions using estimated crossover rates for marker intervals.